Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016031.1 Corchorus capsularis cultivar CVL-1 contig16052, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 179749
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2314 original size:29 final size:29
Alignment explanation
Indices: 2272--2330 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2262 GATGTCTTGG
2272 TTGTCTTGTCTTTAGATCTCCCATGCCCA
1 TTGTCTTGTCTTTAGATCTCCCATGCCCA
2301 TTGTCTTGTCTTTAGATCTCCCATGCCCA
1 TTGTCTTGTCTTTAGATCTCCCATGCCCA
2330 T
1 T
2331 CATTTCCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.42
Consensus pattern (29 bp):
TTGTCTTGTCTTTAGATCTCCCATGCCCA
Found at i:6847 original size:25 final size:26
Alignment explanation
Indices: 6811--6861 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
6801 CAGTACAATC
6811 TACAGATATACTATATACTA-TACTA
1 TACAGATATACTATATACTATTACTA
*
6836 TACA-ATACTACTATATATTATTACTA
1 TACAGATA-TACTATATACTATTACTA
6862 GTTACTAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 15 0.65
26 5 0.22
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.39
Consensus pattern (26 bp):
TACAGATATACTATATACTATTACTA
Found at i:8701 original size:25 final size:25
Alignment explanation
Indices: 8673--8726 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
8663 AATTTAATAT
*
8673 ATTTAAAATTTAAAAACTATAATTA
1 ATTTAAAATTTAAAAAATATAATTA
8698 ATTTAAAATTTAAAAAATATAATTA
1 ATTTAAAATTTAAAAAATATAATTA
8723 ATTT
1 ATTT
8727 GTTTAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTAAAATTTAAAAAATATAATTA
Found at i:10329 original size:28 final size:28
Alignment explanation
Indices: 10295--10350 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
10285 GCCCTCCAGC
10295 TTTTACGGTAACCTGACATTGCCCTGCT
1 TTTTACGGTAACCTGACATTGCCCTGCT
*
10323 TTTTACGGTAATCTGACATTGCCCTGCT
1 TTTTACGGTAACCTGACATTGCCCTGCT
10351 CCTCCTCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTTACGGTAACCTGACATTGCCCTGCT
Found at i:16293 original size:12 final size:12
Alignment explanation
Indices: 16268--16312 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 12
16258 TCATATAGCA
16268 AATATATATAATAT
1 AATATA-AT-ATAT
16282 AATATAATATAT
1 AATATAATATAT
16294 AATATAATTACTAT
1 AATATAA-TA-TAT
16308 AATAT
1 AATAT
16313 GGGTACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.38
13 4 0.14
14 14 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATAATATAT
Found at i:18720 original size:12 final size:12
Alignment explanation
Indices: 18703--18727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18693 ATAATTATTG
18703 TGTTTTATTTTA
1 TGTTTTATTTTA
18715 TGTTTTATTTTA
1 TGTTTTATTTTA
18727 T
1 T
18728 TTATATATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TGTTTTATTTTA
Found at i:25637 original size:31 final size:31
Alignment explanation
Indices: 25589--25669 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
25579 AGTTTTAAGA
*
25589 AACTTTTGAAT-TGTCTATTGTACCCTTAATT
1 AACTTTT-AATATTTCTATTGTACCCTTAATT
25620 AACTTTTAATATTTCTATTGTACCCTTAATT
1 AACTTTTAATATTTCTATTGTACCCTTAATT
*
25651 AACTATTAATATTTCTATT
1 AACTTTTAATATTTCTATT
25670 ATATCGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 3 0.06
31 44 0.94
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.51
Consensus pattern (31 bp):
AACTTTTAATATTTCTATTGTACCCTTAATT
Found at i:26173 original size:31 final size:31
Alignment explanation
Indices: 26125--26185 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
26115 AGTTTTGAGA
*
26125 AACTTTTGAAATACCTATTGTACCCTTATTT
1 AACTTTTGAAATACCTATTATACCCTTATTT
* *
26156 AACTTTT-AATATTCCTATTATATCCTTATT
1 AACTTTTGAA-ATACCTATTATACCCTTATT
26186 AGTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.49
Consensus pattern (31 bp):
AACTTTTGAAATACCTATTATACCCTTATTT
Found at i:28130 original size:16 final size:16
Alignment explanation
Indices: 28094--28124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28084 ATGTCGAATC
*
28094 ATTTGGGTTTGGGTCA
1 ATTTTGGTTTGGGTCA
28110 ATTTTGGTTTGGGTC
1 ATTTTGGTTTGGGTC
28125 TTTTTTAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.35, T:0.48
Consensus pattern (16 bp):
ATTTTGGTTTGGGTCA
Found at i:28135 original size:16 final size:16
Alignment explanation
Indices: 28100--28142 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28090 AATCATTTGG
*
28100 GTTTGGGTCAATTTTG
1 GTTTGGGTCAATTTTA
**
28116 GTTTGGGTCTTTTTTA
1 GTTTGGGTCAATTTTA
28132 GTTTCGGGTCA
1 GTTT-GGGTCA
28143 TATGGTTCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.09, C:0.09, G:0.30, T:0.51
Consensus pattern (16 bp):
GTTTGGGTCAATTTTA
Found at i:38020 original size:15 final size:15
Alignment explanation
Indices: 37984--38021 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
37974 CACAGATCAA
*
37984 GATGATCATGAGATT
1 GATGATGATGAGATT
*
37999 GATGATGATGAGTTT
1 GATGATGATGAGATT
38014 GATGATGA
1 GATGATGA
38022 AGTATTGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (15 bp):
GATGATGATGAGATT
Found at i:52985 original size:6 final size:6
Alignment explanation
Indices: 52974--53000 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52964 TTTTGGTCCT
52974 CCAAAA CCAAAA CCAAAA CCAAAA CCA
1 CCAAAA CCAAAA CCAAAA CCAAAA CCA
53001 CCCTAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:54393 original size:16 final size:16
Alignment explanation
Indices: 54325--54393 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
54315 TATTCGGATT
54325 TCGGGTCA-TCTGGGT-
1 TCGGGTCATTC-GGGTC
*
54340 TCGGGTTATTCGGGTC
1 TCGGGTCATTCGGGTC
* ** *
54356 TCGGGCCACACGGGTT
1 TCGGGTCATTCGGGTC
54372 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTC
54388 TCGGGT
1 TCGGGT
54394 TGGGCGAGTC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
15 11 0.26
16 31 0.74
ACGTcount: A:0.07, C:0.23, G:0.39, T:0.30
Consensus pattern (16 bp):
TCGGGTCATTCGGGTC
Found at i:54670 original size:42 final size:42
Alignment explanation
Indices: 54618--54699 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
54608 TAGATATTAA
* * *
54618 TTTTGAATATTAAATACATAATCGATTATCAGGTGAGGTAGG
1 TTTTAAATATTAAATACATAATCAATTATCAAGTGAGGTAGG
* *
54660 TTTTAAATATTAAATACATAATTAATTATCAAGTGGGGTA
1 TTTTAAATATTAAATACATAATCAATTATCAAGTGAGGTA
54700 TGCGTCAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (42 bp):
TTTTAAATATTAAATACATAATCAATTATCAAGTGAGGTAGG
Found at i:55256 original size:16 final size:15
Alignment explanation
Indices: 55230--55323 Score: 82
Period size: 16 Copynumber: 5.9 Consensus size: 15
55220 GGTTAACTTC
55230 TCGGGTTTCGGGTCA
1 TCGGGTTTCGGGTCA
*
55245 TACGGGTCTCGGGTCA
1 T-CGGGTTTCGGGTCA
*
55261 CTCAGGTTTCGGGTCA
1 -TCGGGTTTCGGGTCA
*
55277 TTCGGATTTCGGGTCA
1 -TCGGGTTTCGGGTCA
*
55293 TC-TGTATTACGGGTCA
1 TCGGGT-TT-CGGGTCA
*
55309 TTCGGGTCTCGGGTC
1 -TCGGGTTTCGGGTC
55324 GGGCAGATTC
Statistics
Matches: 63, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
14 1 0.02
15 5 0.08
16 51 0.81
17 4 0.06
18 2 0.03
ACGTcount: A:0.11, C:0.22, G:0.34, T:0.33
Consensus pattern (15 bp):
TCGGGTTTCGGGTCA
Found at i:55274 original size:32 final size:30
Alignment explanation
Indices: 55233--55323 Score: 110
Period size: 32 Copynumber: 2.9 Consensus size: 30
55223 TAACTTCTCG
*
55233 GGTTTCGGGTCATACGGGTCTCGGGTCACTC
1 GGTTTCGGGTCATTCGGGTCTCGGGTCA-TC
* *
55264 AGGTTTCGGGTCATTCGGATTTCGGGTCATC
1 -GGTTTCGGGTCATTCGGGTCTCGGGTCATC
*
55295 TGTATTACGGGTCATTCGGGTCTCGGGTC
1 GGT-TT-CGGGTCATTCGGGTCTCGGGTC
55324 GGGCAGATTC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 4 0.08
32 45 0.88
ACGTcount: A:0.11, C:0.22, G:0.34, T:0.33
Consensus pattern (30 bp):
GGTTTCGGGTCATTCGGGTCTCGGGTCATC
Found at i:57033 original size:2 final size:2
Alignment explanation
Indices: 57026--57056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57016 TAATATGTAG
57026 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57057 TAGTATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58066 original size:22 final size:22
Alignment explanation
Indices: 58041--58089 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
58031 ATTTTTATTC
58041 TAAAACCCTACGGGGAATGTAT
1 TAAAACCCTACGGGGAATGTAT
***
58063 TAAAATTTTACGGGGAATGTAT
1 TAAAACCCTACGGGGAATGTAT
58085 TAAAA
1 TAAAA
58090 TTTAGAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (22 bp):
TAAAACCCTACGGGGAATGTAT
Found at i:58090 original size:22 final size:22
Alignment explanation
Indices: 58049--58092 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
58039 TCTAAAACCC
58049 TACGGGGAATGTATTAAAATTT
1 TACGGGGAATGTATTAAAATTT
58071 TACGGGGAATGTATTAAAATTT
1 TACGGGGAATGTATTAAAATTT
58093 AGAACTCACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (22 bp):
TACGGGGAATGTATTAAAATTT
Found at i:66366 original size:41 final size:41
Alignment explanation
Indices: 66321--66403 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
66311 AACTATTAAA
66321 TTGCTTAACACAATTCAATATAAAAATACCAGGTTTCGGAG
1 TTGCTTAACACAATTCAATATAAAAATACCAGGTTTCGGAG
* *
66362 TTGCTTAACAGAATTCAATATAAAAATACCAGGTTTTGGAG
1 TTGCTTAACACAATTCAATATAAAAATACCAGGTTTCGGAG
66403 T
1 T
66404 GGGAGGAGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (41 bp):
TTGCTTAACACAATTCAATATAAAAATACCAGGTTTCGGAG
Found at i:66762 original size:6 final size:6
Alignment explanation
Indices: 66753--66779 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
66743 CAGCAGCAGC
66753 GCGAGG GCGAGG GCGAGG GCGAGG GCG
1 GCGAGG GCGAGG GCGAGG GCGAGG GCG
66780 TGGAGCTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.19, G:0.67, T:0.00
Consensus pattern (6 bp):
GCGAGG
Found at i:68549 original size:7 final size:7
Alignment explanation
Indices: 68537--68566 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
68527 TTCCCTGCTA
68537 GACTAGT
1 GACTAGT
68544 GACTAGT
1 GACTAGT
68551 GACTAGT
1 GACTAGT
*
68558 AACTAGT
1 GACTAGT
68565 GA
1 GA
68567 GAACCTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (7 bp):
GACTAGT
Found at i:83854 original size:23 final size:23
Alignment explanation
Indices: 83815--83867 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
83805 GAAAAAAAAT
83815 AAAAAAAGGAAAGAAATAGAAAG
1 AAAAAAAGGAAAGAAATAGAAAG
*
83838 AAAAATAAGGAAA-AAATGGAAAG
1 AAAAA-AAGGAAAGAAATAGAAAG
83861 AAAAAAA
1 AAAAAAA
83868 CAGGAACAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 2 0.07
23 19 0.68
24 7 0.25
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (23 bp):
AAAAAAAGGAAAGAAATAGAAAG
Found at i:83872 original size:24 final size:24
Alignment explanation
Indices: 83815--83873 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
83805 GAAAAAAAAT
83815 AAAAAAAGGAAAGAAATAGAAAGA
1 AAAAAAAGGAAAGAAATAGAAAGA
* *
83839 AAAATAAGGAAA-AAATGGAAAGA
1 AAAAAAAGGAAAGAAATAGAAAGA
83862 AAAAAACAGGAA
1 AAAAAA-AGGAA
83874 CAGTCAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (24 bp):
AAAAAAAGGAAAGAAATAGAAAGA
Found at i:90018 original size:24 final size:24
Alignment explanation
Indices: 89991--90063 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
89981 GTAAGCAATG
*
89991 TGCTTTGTCATTGTATATTGGATA
1 TGCTTTGTCATTATATATTGGATA
90015 TGCTTTGTCATTATATATTGGATA
1 TGCTTTGTCATTATATATTGGATA
*
90039 TGCTATGTCATTATATATTGGATA
1 TGCTTTGTCATTATATATTGGATA
90063 T
1 T
90064 CTGGAAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (24 bp):
TGCTTTGTCATTATATATTGGATA
Found at i:99726 original size:20 final size:20
Alignment explanation
Indices: 99703--99742 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
99693 ATTTATATGA
*
99703 AACATACTAAATATATATTT
1 AACATACTAAATATAGATTT
*
99723 AACATATTAAATATAGATTT
1 AACATACTAAATATAGATTT
99743 TTTATTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (20 bp):
AACATACTAAATATAGATTT
Found at i:110226 original size:15 final size:16
Alignment explanation
Indices: 110193--110228 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
110183 TGGATTATTA
110193 AATAATGGATGCTAAT
1 AATAATGGATGCTAAT
*
110209 AATAATGGATTC-AAT
1 AATAATGGATGCTAAT
110224 AATAA
1 AATAA
110229 AATGGGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.31
Consensus pattern (16 bp):
AATAATGGATGCTAAT
Found at i:111024 original size:1 final size:1
Alignment explanation
Indices: 111018--111044 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
111008 TGGCAGCTGT
111018 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
111045 CTCATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:111576 original size:7 final size:7
Alignment explanation
Indices: 111564--111591 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
111554 TTTTGGTCTC
111564 CCTCAGG
1 CCTCAGG
111571 CCTCAGG
1 CCTCAGG
111578 CCTCAGG
1 CCTCAGG
111585 CCTCAGG
1 CCTCAGG
111592 TAATCTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (7 bp):
CCTCAGG
Found at i:113372 original size:20 final size:20
Alignment explanation
Indices: 113349--113391 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
113339 TACAAAAATG
*
113349 ATAATATTAT-TATATTAACA
1 ATAATATTATAAATATTAA-A
113369 ATAATATTATAAATATTAAA
1 ATAATATTATAAATATTAAA
113389 ATA
1 ATA
113392 TTGTATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATATTATAAATATTAAA
Found at i:116609 original size:19 final size:19
Alignment explanation
Indices: 116581--116630 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
116571 TTGTGTCTCA
116581 TATATATCTATATCTAT-C
1 TATATATCTATATCTATAC
116599 TATACTATCTATATCTATAC
1 TATA-TATCTATATCTATAC
116619 TA-ATTATCTATA
1 TATA-TATCTATA
116631 CTAATTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 4 0.14
19 22 0.76
20 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATATCTATATCTATAC
Found at i:116634 original size:13 final size:13
Alignment explanation
Indices: 116595--116638 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
116585 TATCTATATC
*
116595 TATCTATACTATCT
1 TATCTATACTA-AT
116609 ATATCTATACTAAT
1 -TATCTATACTAAT
116623 TATCTATACTAAT
1 TATCTATACTAAT
116636 TAT
1 TAT
116639 AACGTGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 16 0.57
14 1 0.04
15 11 0.39
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TATCTATACTAAT
Found at i:116919 original size:31 final size:31
Alignment explanation
Indices: 116858--116919 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
116848 GGTTTTGTAA
** *
116858 AACTTTTGAAACGTCTATTGTACCCTTATTT
1 AACTTTTGAAACGTCTATTACACCCATATTT
* *
116889 AACTTTTGAAATGTCTATTACATCCATATTT
1 AACTTTTGAAACGTCTATTACACCCATATTT
116920 CTCTAACATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (31 bp):
AACTTTTGAAACGTCTATTACACCCATATTT
Found at i:125754 original size:11 final size:11
Alignment explanation
Indices: 125738--125762 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
125728 TACTAAAAAT
125738 TCTTTAATATA
1 TCTTTAATATA
125749 TCTTTAATATA
1 TCTTTAATATA
125760 TCT
1 TCT
125763 AGATCAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTTTAATATA
Found at i:137789 original size:15 final size:15
Alignment explanation
Indices: 137766--137795 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
137756 TTGAACCTTC
137766 AAAAAAAAACAAAAT
1 AAAAAAAAACAAAAT
*
137781 AAAACAAAACAAAAT
1 AAAAAAAAACAAAAT
137796 TCTTGATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (15 bp):
AAAAAAAAACAAAAT
Found at i:139869 original size:4 final size:4
Alignment explanation
Indices: 139862--139902 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
139852 ATATATATAA
*
139862 AAAT AAAT AAAT AAAT AAAT -AAT AAAT -ACT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
139903 CCTCATCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 5 0.15
4 28 0.85
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:139894 original size:18 final size:19
Alignment explanation
Indices: 139858--139901 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
139848 ATTTATATAT
139858 ATAAA-AATAAATAAATAA
1 ATAAATAATAAATAAATAA
*
139876 ATAAATAATAAAT-ACTAA
1 ATAAATAATAAATAAATAA
139894 ATAAATAA
1 ATAAATAA
139902 ACCTCATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAATAATAAATAAATAA
Found at i:145831 original size:95 final size:96
Alignment explanation
Indices: 145714--145905 Score: 341
Period size: 95 Copynumber: 2.0 Consensus size: 96
145704 TCAGTCCAAA
*
145714 TAGCTGATTGTAAATGGCAAAAGAAACTAACAGCATTTGCATACAGAAAGGCTAAGAAACTGCAC
1 TAGCTGATTATAAATGGCAAAAGAAACTAACAGCATTTGCATACAGAAAGGCTAAGAAACTGCAC
145779 TGAAGAATAACACCAAAACTAAGGAAATCAT
66 TGAAGAATAACACCAAAACTAAGGAAATCAT
* *
145810 TAGCTGA-TATAAATGGCAAAAGGAACTAACAGCATTTGCATACAGAAAGGCTAAGAAACTGCAT
1 TAGCTGATTATAAATGGCAAAAGAAACTAACAGCATTTGCATACAGAAAGGCTAAGAAACTGCAC
*
145874 TGAAGAATAACACCAAAGCTAAGGAAATCAT
66 TGAAGAATAACACCAAAACTAAGGAAATCAT
145905 T
1 T
145906 TTTTCGACAA
Statistics
Matches: 92, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
95 85 0.92
96 7 0.08
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.19
Consensus pattern (96 bp):
TAGCTGATTATAAATGGCAAAAGAAACTAACAGCATTTGCATACAGAAAGGCTAAGAAACTGCAC
TGAAGAATAACACCAAAACTAAGGAAATCAT
Found at i:148498 original size:1 final size:1
Alignment explanation
Indices: 148492--148533 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
148482 TGTCAACTTT
148492 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
148534 GGTTTTCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:151071 original size:2 final size:2
Alignment explanation
Indices: 151064--151091 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
151054 TAAATATTGA
151064 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151092 CAATTTACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:153825 original size:2 final size:2
Alignment explanation
Indices: 153818--153851 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
153808 ATTATAAAAG
153818 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
153852 TTGAATAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:157104 original size:14 final size:14
Alignment explanation
Indices: 157087--157118 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
157077 AAGCTTATAT
157087 AGTCTTTTCGTTAC
1 AGTCTTTTCGTTAC
*
157101 AGTCTTTTTGTTAC
1 AGTCTTTTCGTTAC
157115 AGTC
1 AGTC
157119 GCAATTGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.50
Consensus pattern (14 bp):
AGTCTTTTCGTTAC
Found at i:158752 original size:3 final size:3
Alignment explanation
Indices: 158744--158782 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
158734 ATCTATAGTA
158744 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
158783 AATACAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:159758 original size:177 final size:179
Alignment explanation
Indices: 159416--159775 Score: 573
Period size: 182 Copynumber: 2.0 Consensus size: 179
159406 TTCATGAAAG
**
159416 TTGTAGACCATAGAAATACCTTTAAATAGACATTTAAATCACCTTGATCGGTCAAATAGAAAAAA
1 TTGTAGACCATAGAAATACCTTTAAATAGACACCTAAATCACCTTGATCGGTCAAATAG--AAAA
* * *
159481 AATAAAAGAATTAAAGCTGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGTAT
64 AATAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCAT
*
159546 AAATTATAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAAATGA
129 AAATTAGAAAAGTATGAGGATCATTTAATAAATAATCCAAC-AAAAAAATGA
* * * *
159598 TTGTCGACCATGGAATTACCTTTAAATAGACACCTGAATCACCTTGATCGGTCAAATAG-AAAAA
1 TTGTAGACCATAGAAATACCTTTAAATAGACACCTAAATCACCTTGATCGGTCAAATAGAAAAAA
*
159662 -AAAACAATTAAAGCCGAAACATTCAATCGTCCAACATATAATTGTAAG-GATTAAATAGCATAA
66 TAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCATAA
159725 ATTAGAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
131 ATTAGAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
159774 TT
1 TT
159776 TGTTTATGGA
Statistics
Matches: 167, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
176 12 0.07
177 52 0.31
178 45 0.27
179 5 0.03
182 53 0.32
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (179 bp):
TTGTAGACCATAGAAATACCTTTAAATAGACACCTAAATCACCTTGATCGGTCAAATAGAAAAAA
TAAAACAATTAAAGCCGAAACATTCAATCGTCCAACACATAATTGTAAGTGATTAAATAGCATAA
ATTAGAAAAGTATGAGGATCATTTAATAAATAATCCAACAAAAAAATGA
Found at i:164638 original size:2 final size:2
Alignment explanation
Indices: 164631--164665 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
164621 CTTATTAGGG
164631 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
164666 AAAATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:165423 original size:2 final size:2
Alignment explanation
Indices: 165418--165456 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
165408 AGTGTGTGTG
165418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
165457 GTATTTAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:165536 original size:20 final size:22
Alignment explanation
Indices: 165511--165560 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
165501 TTTTATGAAA
165511 TTTGATAA-T-CAATATAAAAT
1 TTTGATAATTACAATATAAAAT
*
165531 TTTGATAATTACACTATAAAAT
1 TTTGATAATTACAATATAAAAT
*
165553 TTTTATAA
1 TTTGATAA
165561 CGATACAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 17 0.65
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (22 bp):
TTTGATAATTACAATATAAAAT
Found at i:165614 original size:22 final size:22
Alignment explanation
Indices: 165584--165644 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
165574 TTTCGAGAAT
*
165584 CTCCATATGAAATTTTGTTA-A
1 CTCCCTATGAAATTTTGTTACA
165605 CTTCCCTATGAAATTTTGTTACA
1 C-TCCCTATGAAATTTTGTTACA
*
165628 CTCCCTATAAAAATTTT
1 CTCCCTAT-GAAATTTT
165645 AATAATTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 25 0.71
23 9 0.26
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.43
Consensus pattern (22 bp):
CTCCCTATGAAATTTTGTTACA
Found at i:165692 original size:22 final size:21
Alignment explanation
Indices: 165650--165724 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
165640 ATTTTAATAA
* *
165650 TTTGATAATCACCTATGAAAT
1 TTTGATAATCCCCAATGAAAT
165671 TTTGATAATCTCCCAATGAAAT
1 TTTGATAATC-CCCAATGAAAT
* * * *
165693 GTTGGTAAGCGCACATTATGAAAT
1 TTTGATAATC-CCCA--ATGAAAT
165717 TTTGATAA
1 TTTGATAA
165725 CCTTTCGATA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
21 10 0.24
22 19 0.45
24 13 0.31
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
TTTGATAATCCCCAATGAAAT
Found at i:165779 original size:22 final size:20
Alignment explanation
Indices: 165754--165986 Score: 108
Period size: 22 Copynumber: 10.8 Consensus size: 20
165744 TAATTACATT
165754 ATGAAATTTTGATAACCATACC
1 ATGAAATTTTGATAACC-T-CC
*
165776 ATGAAATTGTGAT-ACCTCAC
1 ATGAAATTTTGATAACCTC-C
* *
165796 TATGAAATTTTTATAAAGCTCCC
1 -ATGAAATTTTGAT-AACCT-CC
* *
165819 TATAAAATTTTGATAACTTCC
1 -ATGAAATTTTGATAACCTCC
* * *
165840 AATTGAAATTTTTAAAACCATCTT
1 -A-TGAAATTTTGATAACC-TC-C
*
165864 ATGAAATTTTGATAACATCC
1 ATGAAATTTTGATAACCTCC
* * *
165884 ATATAAATTTTTTATAACCTTCTT
1 AT-GAAA-TTTTGATAACC-TC-C
* *
165908 ATAAAATTTTGTTAACCTCC
1 ATGAAATTTTGATAACCTCC
* * * *
165928 TACGAAATTTTGATAAGAACACT
1 -ATGAAATTTTGAT-A-ACCTCC
* *
165951 ATTAAATTTTGATAACCCCC
1 ATGAAATTTTGATAACCTCC
165971 AATGAAATTTTGATAA
1 -ATGAAATTTTGATAA
165987 TTAACTACAC
Statistics
Matches: 157, Mismatches: 38, Indels: 33
0.69 0.17 0.14
Matches are distributed among these distances:
19 1 0.01
20 7 0.04
21 49 0.31
22 70 0.45
23 27 0.17
24 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (20 bp):
ATGAAATTTTGATAACCTCC
Found at i:165872 original size:44 final size:43
Alignment explanation
Indices: 165779--165981 Score: 157
Period size: 44 Copynumber: 4.7 Consensus size: 43
165769 CCATACCATG
* * * *
165779 AAATTGTGAT-ACCTCACTATGAAATTTTTATAAAGC-TCCCTATA
1 AAATTTTGATAACCTC-CAATGAAATTTTTA-AAACCAT-CTTATA
* *
165823 AAATTTTGATAACTTCCAATTGAAATTTTTAAAACCATCTTATG
1 AAATTTTGATAACCTCCAA-TGAAATTTTTAAAACCATCTTATA
* * *
165867 AAATTTTGATAACATCCATAT-AAATTTTTTATAACCTTCTTATA
1 AAATTTTGATAACCTCCA-ATGAAA-TTTTTAAAACCATCTTATA
* * * *
165911 AAATTTTGTTAACCTCCTACGAAATTTTGATAAGAA-CA-C-TATT
1 AAATTTTGATAACCTCCAATGAAATTTT--TAA-AACCATCTTATA
*
165954 AAATTTTGATAACCCCCAATGAAATTTT
1 AAATTTTGATAACCTCCAATGAAATTTT
165982 GATAATTAAC
Statistics
Matches: 129, Mismatches: 21, Indels: 19
0.76 0.12 0.11
Matches are distributed among these distances:
43 35 0.27
44 72 0.56
45 20 0.16
46 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (43 bp):
AAATTTTGATAACCTCCAATGAAATTTTTAAAACCATCTTATA
Found at i:166093 original size:21 final size:22
Alignment explanation
Indices: 166067--166143 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
166057 CCACACAATC
* *
166067 AAATTTTGTTAATCTCACTAT-
1 AAATTTTGATAAACTCACTATG
*
166088 AAATTTTGATAAACTCATTATG
1 AAATTTTGATAAACTCACTATG
* * * * *
166110 AAATTTTAATCACCACACAATG
1 AAATTTTGATAAACTCACTATG
*
166132 AAAATTTGATAA
1 AAATTTTGATAA
166144 CCTCTGCCTC
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
21 18 0.42
22 25 0.58
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAAACTCACTATG
Found at i:166116 original size:22 final size:21
Alignment explanation
Indices: 166067--166116 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
166057 CCACACAATC
* *
166067 AAATTTTGTTAATCTCACTAT
1 AAATTTTGATAAACTCACTAT
*
166088 AAATTTTGATAAACTCATTAT
1 AAATTTTGATAAACTCACTAT
166109 GAAATTTT
1 -AAATTTT
166117 AATCACCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (21 bp):
AAATTTTGATAAACTCACTAT
Found at i:166244 original size:22 final size:22
Alignment explanation
Indices: 166194--166256 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
166184 CATATATACT
*
166194 ATGAAATTGTGATAATCTCCCTC
1 ATGAAATT-TGATAACCTCCCTC
*
166217 -TAAAATTTCGATAACCTCCC-C
1 ATGAAATTT-GATAACCTCCCTC
*
166238 ATGAAATTTTGTTAACCTC
1 ATGAAA-TTTGATAACCTC
166257 TATGAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.06
22 28 0.85
23 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.35
Consensus pattern (22 bp):
ATGAAATTTGATAACCTCCCTC
Found at i:166384 original size:22 final size:22
Alignment explanation
Indices: 166355--166659 Score: 140
Period size: 22 Copynumber: 13.6 Consensus size: 22
166345 ATAAGCACAC
*
166355 TATGAAATTTTGATAATCTCCA
1 TATGAAATTTTGATAACCTCCA
* ** * * *
166377 TATAAAATTTCAATAATCGCCT
1 TATGAAATTTTGATAACCTCCA
**
166399 TATGAAATTTTGATAA-CTAGA
1 TATGAAATTTTGATAACCTCCA
* *
166420 GCATGAAATTTT-AGTAACCTCCT
1 -TATGAAATTTTGA-TAACCTCCA
*
166443 TGTGAAATTTTGATAACCTTCC-
1 TATGAAATTTTGATAACC-TCCA
* * *
166465 CATG-AATTTCGATAACCTCCT
1 TATGAAATTTTGATAACCTCCA
*
166486 TATGAAATTTTGATAAACTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
166508 TATGAAATTTTGATGACAATATCA
1 TATGAAATTTTGATAAC-CT-CCA
* *
166532 TTATGAAATTTTATTTTAATAACCTCCT
1 -TATG-AA----ATTTTGATAACCTCCA
*
166560 TATGAAATTTTGATAACATCC-
1 TATGAAATTTTGATAACCTCCA
* * *
166581 CATGAAATTGTGATAA-CTACAA
1 TATGAAATTTTGATAACCT-CCA
* * * *
166603 TATAAAATTTTAATATCATACC-
1 TATGAAATTTTGATAACCT-CCA
* *
166625 TATGAAATTTTGGTAACC-ACA
1 TATGAAATTTTGATAACCTCCA
*
166646 CTATAAAATTTTGA
1 -TATGAAATTTTGA
166660 GAATCACACT
Statistics
Matches: 208, Mismatches: 55, Indels: 40
0.69 0.18 0.13
Matches are distributed among these distances:
20 5 0.02
21 32 0.15
22 136 0.65
23 10 0.05
24 2 0.01
25 4 0.02
26 4 0.02
27 4 0.02
28 1 0.00
29 1 0.00
30 9 0.04
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:166403 original size:44 final size:43
Alignment explanation
Indices: 166355--166517 Score: 168
Period size: 44 Copynumber: 3.7 Consensus size: 43
166345 ATAAGCACAC
* * * *
166355 TATGAAATTTTGATAATCTCCATATAAAATTTCAATAATCGCCT
1 TATGAAATTTTGATAA-CTCCACATGAAATTTCAATAACCTCCT
** * *
166399 TATGAAATTTTGATAACTAGAGCATGAAATTTTAGTAACCTCCT
1 TATGAAATTTTGATAACTCCA-CATGAAATTTCAATAACCTCCT
* *
166443 TGTGAAATTTTGATAACCTTCC-CATG-AATTTCGATAACCTCCT
1 TATGAAATTTTGATAA-C-TCCACATGAAATTTCAATAACCTCCT
*
166486 TATGAAATTTTGATAAACTCCATATGAAATTT
1 TATGAAATTTTGAT-AACTCCACATGAAATTT
166518 TGATGACAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
42 3 0.03
43 34 0.35
44 58 0.60
45 1 0.01
46 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACTCCACATGAAATTTCAATAACCTCCT
Found at i:166490 original size:21 final size:22
Alignment explanation
Indices: 166355--166597 Score: 145
Period size: 22 Copynumber: 10.8 Consensus size: 22
166345 ATAAGCACAC
* *
166355 TATGAAATTTTGATAATCTCCA
1 TATGAAATTTTGATAACCTCCT
* ** * *
166377 TATAAAATTTCAATAATCGCCT
1 TATGAAATTTTGATAACCTCCT
***
166399 TATGAAATTTTGATAA-CTAGAG
1 TATGAAATTTTGATAACCT-CCT
*
166421 CATGAAATTTT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCCT
*
166443 TGTGAAATTTTGATAACCTTCC-
1 TATGAAATTTTGATAACC-TCCT
* *
166465 CATG-AATTTCGATAACCTCCT
1 TATGAAATTTTGATAACCTCCT
* *
166486 TATGAAATTTTGATAAACTCCA
1 TATGAAATTTTGATAACCTCCT
** *
166508 TATGAAATTTTGATGACAATATCAT
1 TATGAAATTTTGAT---AACCTCCT
*
166533 TATGAAATTTTATTTTAATAACCTCCT
1 TATG-AA----ATTTTGATAACCTCCT
*
166560 TATGAAATTTTGATAACATCC-
1 TATGAAATTTTGATAACCTCCT
* *
166581 CATGAAATTGTGATAAC
1 TATGAAATTTTGATAAC
166598 TACAATATAA
Statistics
Matches: 169, Mismatches: 37, Indels: 31
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.02
21 32 0.19
22 100 0.59
23 6 0.04
25 8 0.05
26 4 0.02
27 9 0.05
30 7 0.04
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCT
Found at i:166651 original size:44 final size:44
Alignment explanation
Indices: 166564--166687 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 44
166554 CCTCCTTATG
* * * * * *
166564 AAATTTTGATAACAT-CCCATGAAATTGTGATAACTACAATATA
1 AAATTTTAATATCATACCTATGAAATTTTGGTAACCACAATATA
*
166607 AAATTTTAATATCATACCTATGAAATTTTGGTAACCACACTATA
1 AAATTTTAATATCATACCTATGAAATTTTGGTAACCACAATATA
* * *
166651 AAATTTTGAGA-ATCACA-CTATAAAATTTTAGTAACCA
1 AAATTTT-A-ATATCATACCTATGAAATTTTGGTAACCA
166688 AAGAATAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
43 13 0.19
44 48 0.71
45 6 0.09
46 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (44 bp):
AAATTTTAATATCATACCTATGAAATTTTGGTAACCACAATATA
Found at i:166667 original size:22 final size:22
Alignment explanation
Indices: 166603--166679 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
166593 ATAACTACAA
*
166603 TATAAAATTTT-A-ATATCATACC
1 TATAAAATTTTGAGA-ATCACA-C
* *
166625 TATGAAATTTTG-GTAACCACAC
1 TATAAAATTTTGAG-AATCACAC
166647 TATAAAATTTTGAGAATCACAC
1 TATAAAATTTTGAGAATCACAC
166669 TATAAAATTTT
1 TATAAAATTTT
166680 AGTAACCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
22 40 0.87
23 5 0.11
24 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (22 bp):
TATAAAATTTTGAGAATCACAC
Found at i:167217 original size:28 final size:28
Alignment explanation
Indices: 167185--167240 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
167175 CATTGTTTTA
167185 TTCTCTATATTCAATTAATTGAAAGAGT
1 TTCTCTATATTCAATTAATTGAAAGAGT
167213 TTCTCTATATTCAATTAATTGAAAGAGT
1 TTCTCTATATTCAATTAATTGAAAGAGT
167241 CGTCGAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (28 bp):
TTCTCTATATTCAATTAATTGAAAGAGT
Found at i:168049 original size:2 final size:2
Alignment explanation
Indices: 167999--168032 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
167989 TTCGTACTTT
*
167999 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
168033 GACTTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:168479 original size:21 final size:20
Alignment explanation
Indices: 168441--168480 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
168431 ACAAATATAG
* *
168441 GGGTTTTCTTTTTGAGAAAT
1 GGGTTTTATTTTTAAGAAAT
168461 GGGTATTTATTTTTAAGAAA
1 GGGT-TTTATTTTTAAGAAA
168481 AATATAAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (20 bp):
GGGTTTTATTTTTAAGAAAT
Found at i:168757 original size:25 final size:24
Alignment explanation
Indices: 168726--168788 Score: 101
Period size: 24 Copynumber: 2.6 Consensus size: 24
168716 ATAATGAATG
168726 AAAATTGATTTTTTTTTTCACAAAA
1 AAAATTGATTTTTTTTTTCAC-AAA
168751 AAAATTGA-TTTTTTTTTCACAAA
1 AAAATTGATTTTTTTTTTCACAAA
*
168774 AAAATTGATGTTTTT
1 AAAATTGATTTTTTT
168789 CCCTAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
23 11 0.31
24 17 0.47
25 8 0.22
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (24 bp):
AAAATTGATTTTTTTTTTCACAAA
Found at i:168762 original size:24 final size:23
Alignment explanation
Indices: 168726--168788 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
168716 ATAATGAATG
168726 AAAATTGATTTTTTTTTTCACAAAA
1 AAAATTGA-TTTTTTTTTCAC-AAA
168751 AAAATTGATTTTTTTTTCACAAA
1 AAAATTGATTTTTTTTTCACAAA
*
168774 AAAATTGATGTTTTT
1 AAAATTGATTTTTTT
168789 CCCTAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 17 0.46
24 12 0.32
25 8 0.22
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (23 bp):
AAAATTGATTTTTTTTTCACAAA
Found at i:168797 original size:23 final size:22
Alignment explanation
Indices: 168739--168800 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
168729 ATTGATTTTT
*
168739 TTTTTCACAAAAAAAATTGATTTT
1 TTTTTCACAAAAAAAATTGA--TG
168763 TTTTTCAC-AAAAAAATTGATG
1 TTTTTCACAAAAAAAATTGATG
* *
168784 TTTTTCCCTAAAAAAAT
1 TTTTTCACAAAAAAAAT
168801 ACATGTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.23
22 8 0.23
23 11 0.31
24 8 0.23
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (22 bp):
TTTTTCACAAAAAAAATTGATG
Found at i:168806 original size:22 final size:21
Alignment explanation
Indices: 168763--168806 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
168753 AATTGATTTT
**
168763 TTTTTCACAAAAAAATTGATG
1 TTTTTCACAAAAAAATACATG
*
168784 TTTTTCCCTAAAAAAATACATG
1 TTTTTCAC-AAAAAAATACATG
168806 T
1 T
168807 ATTAAATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCACAAAAAAATACATG
Found at i:169154 original size:23 final size:25
Alignment explanation
Indices: 169125--169175 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
169115 GGCATCTAAA
169125 TTTTTTT-G-AAGATAACGAATACT
1 TTTTTTTGGTAAGATAACGAATACT
169148 TTTTTTTGAGGTAAGATAACGAATACT
1 TTTTTTT--GGTAAGATAACGAATACT
169175 T
1 T
169176 AATTACTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.29
26 1 0.04
27 16 0.67
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (25 bp):
TTTTTTTGGTAAGATAACGAATACT
Found at i:170560 original size:29 final size:29
Alignment explanation
Indices: 170527--170586 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
170517 ATATTTATCT
* * *
170527 TATAATGGGTATTTTTTTTCTAAAATTGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
170556 TATAATGGGTAGTTTTTATCTAAAATGGG
1 TATAATGGGTAGTTTTTATCTAAAATGGG
170585 TA
1 TA
170587 GTTTTTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (29 bp):
TATAATGGGTAGTTTTTATCTAAAATGGG
Found at i:171654 original size:2 final size:2
Alignment explanation
Indices: 171649--171691 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
171639 TATGTGTGTG
* * *
171649 TA TA TA TA TA TA TA TC TA TG TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171691 T
1 T
171692 CTATGTATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:171667 original size:26 final size:26
Alignment explanation
Indices: 171633--171689 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
171623 ACCAAGTACT
* *
171633 TATATCTATGTGTGTGTATATATATA
1 TATATCTATGTGTATATATATATATA
171659 TATATCTATGTGTATATATATATATA
1 TATATCTATGTGTATATATATATATA
171685 TATAT
1 TATAT
171690 ATCTATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (26 bp):
TATATCTATGTGTATATATATATATA
Found at i:171716 original size:26 final size:26
Alignment explanation
Indices: 171633--171703 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 26
171623 ACCAAGTACT
* *
171633 TATATCTATGTGTGTGTATATATATA
1 TATATCTATGTATGTATATATATATA
*
171659 TATATCTATGTGTATATATATATATATA
1 TATATCTA--TGTATGTATATATATATA
171687 TATATCTATGTATGTAT
1 TATATCTATGTATGTAT
171704 GTATGTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.41
28 23 0.59
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (26 bp):
TATATCTATGTATGTATATATATATA
Found at i:177877 original size:2 final size:2
Alignment explanation
Indices: 177867--177905 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
177857 TATAACGGGA
177867 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
177906 TCGACGAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.